In this study, we analysed the Gioia Tauro Plain (Tyrrhenian coast, southern Italy) in terms of hydrostratigraphy and the physicochemical status of groundwater. We investigated the hydrostratigraphic framework of the area identifying a deep aquifer (made by late Miocene succession), an aquitard (consisting of Pliocene clayey and silty deposits) and a shallow aquifer (including Late Pleistocene and Holocene marine and alluvial sediments) using subsoil data (boreholes and geophysics). Our reconstruction showed that the structural geology controls the spatial pattern of the aquitard top and the shallow aquifer thickness. Furthermore, we evaluated the hydraulic conductivity for the shallow aquifer using an empirical method, calibrated by slug tests, obtaining values ranging from 10−4 to 10−5 m/s with a maximum of 10−3 m/s located close to inland dune fields. The piezometric level of the shallow aquifer recorded a significant drop between the 1970s and 2021 (−35 m as the worst value). It is the effect of climate and soil use changes, the latter being the increased water demand for kiwi cultivation. Despite the overexploitation of the shallow aquifer, shallow groundwater is fresh (736 µS/cm as mean electrical conductivity) except for a narrow coastal area where the electrical conductivity is more than 1500 µS/cm, which can be due to the seawater intrusion. What was more complex was the physicochemical status of the deep aquifer characterised by high temperature (up to 25.8 °C) and electrical conductivity up to 10,520 µS/cm along the northern and southern plain boundaries marked by tectonic structures. This issue suggested the dominant role of the local fault system that is likely affecting the deep groundwater flow and its chemical evolution.